I recently tried using sortmerna on a small set of files that I grouped into a Collection. The initial raw reads were trimmed as a collection and the paired reads were input as a collection into sortmerna and I tested filtering with both the paired in and paired out options. When I viewed the unaligned vs the aligned result files, I was surprised to see that the output files were the same in both result files.
I tried a test were I ran one of the paired read sets individually and this did produce the expected results, where the aligned and unaligned result files were different.
I’m hoping to run sortmerna as a larger collection, so I’m hoping this issue can be resolved soon.
Thank you for your time and efforts. Any help is always appreciated.
This sounds very odd!! I’m glad you reported it here.
I’m going to start up a small test to see if I can replicate the issue. If you want to share back your example, that can help too, perhaps there will be a difference in the parameters or the way the inputs are organized that provides more clues about this duplicated result.
Or, if you would at least confirm the issue is happening at UseGalaxy.eu (URL at the top of your browser window) and the version of the tool you are running (top of the tool form) that might be enough. If you are running this tool as part of a published workflow or GTN tutorial, I would be interested in learning which of those as well (the share URL would be great).
Again, thanks for reporting the issue! I was able to reproduce a problem with a Paired Collection input choice. This seems new to me but the developers can confirm, and in any case, likely address it!
You will not need to wait as there is a way to use the tool with paired end reads in a slightly different collection shape that avoids the current problem.
Running SortMeRNA with paired end reads
Start with the reads organized into a List of Pairs collection folder (this is the default shape).
Run the tool Unzip Collection. This splits out forward and reverse reads into two collections.
Choose Paired-end Reads as the type of data (instead of Paired Collection).
Toggle the forward read input section to be for a collection using the folder icon, then choose the collection with (forward) in the name, then do the same for the (reverse).
Run the tool! The outputs will be differentiated correctly for all 4 of the sorting choices.
Please also give this a try and let me know if I missed anything else that may still be going wrong! Thanks for your patience while I was investigating!
